+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31471 | ||||||||||||||||||||||||||||||
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タイトル | Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody chAb-45 (Focused refinement of S-RBD and chAb-45 region) | ||||||||||||||||||||||||||||||
マップデータ | Focused refinement of S-RBD and chAb-45 contact region | ||||||||||||||||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||||||||||||||||||||||||||
生物種 | Severe acute respiratory syndrome coronavirus 2 (ウイルス) / Homo sapiens (ヒト) | ||||||||||||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | ||||||||||||||||||||||||||||||
データ登録者 | Yang TJ / Yu PY / Wu HC / Hsu STD | ||||||||||||||||||||||||||||||
資金援助 | 台湾, 9件
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引用 | ジャーナル: PLoS Pathog / 年: 2021 タイトル: Structure-guided antibody cocktail for prevention and treatment of COVID-19. 著者: Shih-Chieh Su / Tzu-Jing Yang / Pei-Yu Yu / Kang-Hao Liang / Wan-Yu Chen / Chun-Wei Yang / Hsiu-Ting Lin / Mei-Jung Wang / Ruei-Min Lu / Hsien-Cheng Tso / Meng-Jhe Chung / Tzung-Yang Hsieh / ...著者: Shih-Chieh Su / Tzu-Jing Yang / Pei-Yu Yu / Kang-Hao Liang / Wan-Yu Chen / Chun-Wei Yang / Hsiu-Ting Lin / Mei-Jung Wang / Ruei-Min Lu / Hsien-Cheng Tso / Meng-Jhe Chung / Tzung-Yang Hsieh / Yu-Ling Chang / Shin-Chang Lin / Fang-Yu Hsu / Feng-Yi Ke / Yi-Hsuan Wu / Yu-Chyi Hwang / I-Ju Liu / Jian-Jong Liang / Chun-Che Liao / Hui-Ying Ko / Cheng-Pu Sun / Ping-Yi Wu / Jia-Tsrong Jan / Yuan-Chih Chang / Yi-Ling Lin / Mi-Hua Tao / Shang-Te Danny Hsu / Han-Chung Wu / 要旨: Development of effective therapeutics for mitigating the COVID-19 pandemic is a pressing global need. Neutralizing antibodies are known to be effective antivirals, as they can be rapidly deployed to ...Development of effective therapeutics for mitigating the COVID-19 pandemic is a pressing global need. Neutralizing antibodies are known to be effective antivirals, as they can be rapidly deployed to prevent disease progression and can accelerate patient recovery without the need for fully developed host immunity. Here, we report the generation and characterization of a series of chimeric antibodies against the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Some of these antibodies exhibit exceptionally potent neutralization activities in vitro and in vivo, and the most potent of our antibodies target three distinct non-overlapping epitopes within the RBD. Cryo-electron microscopy analyses of two highly potent antibodies in complex with the SARS-CoV-2 spike protein suggested they may be particularly useful when combined in a cocktail therapy. The efficacy of this antibody cocktail was confirmed in SARS-CoV-2-infected mouse and hamster models as prophylactic and post-infection treatments. With the emergence of more contagious variants of SARS-CoV-2, cocktail antibody therapies hold great promise to control disease and prevent drug resistance. | ||||||||||||||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_31471.map.gz | 111.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31471-v30.xml emd-31471.xml | 18.8 KB 18.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31471.png | 103 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31471 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31471 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31471_validation.pdf.gz | 414 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31471_full_validation.pdf.gz | 413.6 KB | 表示 | |
XML形式データ | emd_31471_validation.xml.gz | 6.8 KB | 表示 | |
CIF形式データ | emd_31471_validation.cif.gz | 7.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31471 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31471 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_31471.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Focused refinement of S-RBD and chAb-45 contact region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : Cryo-EM structure of SARS-CoV-2 spike in complex with a neutraliz...
全体 | 名称: Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody chAb-45 (Focused refinement of S-RBD and chAb-45 region) |
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要素 |
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-超分子 #1: Cryo-EM structure of SARS-CoV-2 spike in complex with a neutraliz...
超分子 | 名称: Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody chAb-45 (Focused refinement of S-RBD and chAb-45 region) タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-分子 #1: Spike glycoprotein
分子 | 名称: Spike glycoprotein / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス) |
分子量 | 理論値: 142.236328 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...文字列: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STASALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQEFGSGGY IPEAPRDGQA YVRKDGEWVL LSTFLKGQDN SADIQHSGRP LESRGPFEQK LISEEDLNMH TGHHH HHH |
-分子 #2: RBD-chAb45, Heavy chain
分子 | 名称: RBD-chAb45, Heavy chain / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 49.409348 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: EVQLQQSGPE LVKPGASVKI SCKTSGYTFT EYTIYWVKQS LGKSLEWIGG NNPNNDDTTY KQFFKGKATL TVDKSSSTAY MELRSLTSE DSAVYYCARD GYPYYYALDF WGQGTSVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...文字列: EVQLQQSGPE LVKPGASVKI SCKTSGYTFT EYTIYWVKQS LGKSLEWIGG NNPNNDDTTY KQFFKGKATL TVDKSSSTAY MELRSLTSE DSAVYYCARD GYPYYYALDF WGQGTSVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT CPPCPAPELL GG PSVFLFP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRVVS VLTVLHQDWL NGK EYKCKV SNKALPAPIE KTISKAKGQP REPQVYTLPP SRDELTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT TPPV LDSDG SFFLYSKLTV DKSRWQQGNV FSCSVMHEAL HNHYTQKSLS LSPG |
-分子 #3: RBD-chAb45, Light chain
分子 | 名称: RBD-chAb45, Light chain / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 23.524975 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: DIVMTQSQKF MSTSVGDRVS VTCKSSQNVG TNVAWYQQKP GQSPKALIYS ASYRYSGVPD HFTGSGSGTD FTLTISNVQS ADLAEYFCQ QYNNYPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...文字列: DIVMTQSQKF MSTSVGDRVS VTCKSSQNVG TNVAWYQQKP GQSPKALIYS ASYRYSGVPD HFTGSGSGTD FTLTISNVQS ADLAEYFCQ QYNNYPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 1 mg/mL | ||||||||||||
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緩衝液 | pH: 7.6 構成要素:
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV 詳細: blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 1.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |